← Back to search

Pooled CRISPR screens with imaging on microraft arrays reveals stress granule-regulatory factors.

Emily C Wheeler, Anthony Q Vu, Jaclyn M Einstein, Matthew DiSalvo, Noorsher Ahmed, Eric L Van Nostrand, Alexander A Shishkin, Wenhao Jin, Nancy L Allbritton, Gene W Yeo

Nature methods · 2020 · Vol. 17 (6) · pp. 636-642

PubMed ↗ DOI ↗ PMC full text ↗

Abstract

Genetic screens using pooled CRISPR-based approaches are scalable and inexpensive, but restricted to standard readouts, including survival, proliferation and sortable markers. However, many biologically relevant cell states involve cellular and subcellular changes that are only accessible by microscopic visualization, and are currently impossible to screen with pooled methods. Here we combine pooled CRISPR-Cas9 screening with microraft array technology and high-content imaging to screen image-based phenotypes (CRaft-ID; CRISPR-based microRaft followed by guide RNA identification). By isolating microrafts that contain genetic clones harboring individual guide RNAs (gRNA), we identify RNA-binding proteins (RBPs) that influence the formation of stress granules, the punctate protein-RNA assemblies that form during stress. To automate hit identification, we developed a machine-learning model trained on nuclear morphology to remove unhealthy cells or imaging artifacts. In doing so, we identified and validated previously uncharacterized RBPs that modulate stress granule abundance, highlighting the applicability of our approach to facilitate image-based pooled CRISPR screens.

Linked datasets 1

GSE139815 GSE · via ncbi_elink
GEO ↗

Pooled CRISPR screens with imaging on microRaft arrays reveals stress granule-regulatory factors

Homo sapiens

214 data files
FileTypeSize
EWG17_S14_L003_R1_001.fastq.gz OTHER 50.0 MB
EWG18_S15_L003_R1_001.fastq.gz OTHER 60.6 MB
EWG19_S16_L003_R1_001.fastq.gz OTHER 66.6 MB
EWG20_S17_L003_R1_001.fastq.gz OTHER 63.5 MB
EWG21_S32_L004_R1_001.fastq.gz OTHER 106.4 MB
EWG22_S33_L004_R1_001.fastq.gz OTHER 69.7 MB
SG10_144.fastq OTHER 163.8 KB
SG10_145.fastq OTHER 686.1 KB
SG11_130.fastq OTHER 92.2 KB
SG11_131.fastq OTHER 1.7 MB
SG11_133.fastq OTHER 102.4 KB
SG12_144.fastq OTHER 829.4 KB
SG12_145.fastq OTHER 706.6 KB
SG13_130.fastq OTHER 460.8 KB
SG14_142.fastq OTHER 81.9 KB
SG15_130.fastq OTHER 655.4 KB
SG15_131.fastq OTHER 215.0 KB
SG15_132.fastq OTHER 1.4 MB
SG15_133.fastq OTHER 112.6 KB
SG16_142.fastq OTHER 440.3 KB
SG16_143.fastq OTHER 604.2 KB
SG16_144.fastq OTHER 133.1 KB
SG16_145.fastq OTHER 604.2 KB
SG17_130.fastq OTHER 532.5 KB
SG17_131.fastq OTHER 440.3 KB
SG17_132.fastq OTHER 2.0 MB
SG20_142.fastq OTHER 481.3 KB
SG20_145.fastq OTHER 1.1 MB
SG21_130.fastq OTHER 716.8 KB
SG21_131.fastq OTHER 563.2 KB
SG21_133.fastq OTHER 624.6 KB
SG22_142.fastq OTHER 1.0 MB
SG22_143.fastq OTHER 2.5 MB
SG22_145.fastq OTHER 450.6 KB
SG23_130.fastq OTHER 768.0 KB
SG23_131.fastq OTHER 153.6 KB
SG23_133.fastq OTHER 337.9 KB
SG24_142.fastq OTHER 1.3 MB
SG25_130.fastq OTHER 1.0 MB
SG25_131.fastq OTHER 1.3 MB
SG25_132.fastq OTHER 1.5 MB
SG25_133.fastq OTHER 1.4 MB
SG26_142.fastq OTHER 1.5 MB
SG26_143.fastq OTHER 1.1 MB
SG26_144.fastq OTHER 2.0 MB
SG27_130.fastq OTHER 297.0 KB
SG27_131.fastq OTHER 809.0 KB
SG27_133.fastq OTHER 614.4 KB
SG28_145.fastq OTHER 5.0 MB
SG29_130.fastq OTHER 133.1 KB
SG29_133.fastq OTHER 573.4 KB
SG30_142.fastq OTHER 2.3 MB
SG30_143.fastq OTHER 972.8 KB
SG30_144.fastq OTHER 358.4 KB
SG30_145.fastq OTHER 983.0 KB
SG31_130.fastq OTHER 81.9 KB
SG31_131.fastq OTHER 696.3 KB
SG31_133.fastq OTHER 184.3 KB
SG3_130.fastq OTHER 829.4 KB
SG3_131.fastq OTHER 983.0 KB
SG3_133.fastq OTHER 460.8 KB
SG32_142.fastq OTHER 419.8 KB
SG32_144.fastq OTHER 2.2 MB
SG33_131.fastq OTHER 849.9 KB
SG33_132.fastq OTHER 6.7 MB
SG33_133.fastq OTHER 276.5 KB
SG33_143.fastq OTHER 276.5 KB
SG33_145.fastq OTHER 3.2 MB
SG34_131.fastq OTHER 1.7 MB
SG34_133.fastq OTHER 1.6 MB
SG34_142.fastq OTHER 348.2 KB
SG34_143.fastq OTHER 4.7 MB
SG34_144.fastq OTHER 5.4 MB
SG34_145.fastq OTHER 4.2 MB
SG35_131.fastq OTHER 5.1 MB
SG35_133.fastq OTHER 6.5 MB
SG35_142.fastq OTHER 450.6 KB
SG35_143.fastq OTHER 4.2 MB
SG35_144.fastq OTHER 665.6 KB
SG35_145.fastq OTHER 7.4 MB
SG36_132.fastq OTHER 10.5 MB
SG36_142.fastq OTHER 6.5 MB
SG36_143.fastq OTHER 2.6 MB
SG36_144.fastq OTHER 12.5 MB
SG36_145.fastq OTHER 1.1 MB
SG37_143.fastq OTHER 10.2 MB
SG37_144.fastq OTHER 143.4 KB
SG37_145.fastq OTHER 7.6 MB
SG38_132.fastq OTHER 36.0 MB
SG38_143.fastq OTHER 4.3 MB
SG39_143.fastq OTHER 5.6 MB
SG40_132.fastq OTHER 6.3 MB
SG40_143.fastq OTHER 16.2 MB
SG41_132.fastq OTHER 48.0 MB
SG4_142.fastq OTHER 368.6 KB
SG4_143.fastq OTHER 1.6 MB
SG4_144.fastq OTHER 235.5 KB
SG42_132.fastq OTHER 33.9 MB
SG5_133.fastq OTHER 583.7 KB
SG6_142.fastq OTHER 153.6 KB
SG7_131.fastq OTHER 266.2 KB
SG7_132.fastq OTHER 583.7 KB
SG7_133.fastq OTHER 378.9 KB
SG8_143.fastq OTHER 921.6 KB
SG8_145.fastq OTHER 716.8 KB
SG9_130.fastq OTHER 92.2 KB
SG9_131.fastq OTHER 593.9 KB
SRR10384085_GSM4146769 OTHER 50.0 MB
SRR10384086_GSM4146770 OTHER 60.0 MB
SRR10384087_GSM4146771 OTHER 66.0 MB
SRR10384088_GSM4146772 OTHER 63.0 MB
SRR10384089_GSM4146773 OTHER 106.0 MB
SRR10384090_GSM4146774 OTHER 69.0 MB
SRR10384091_GSM4146775 OTHER 5.0 MB
SRR10384092_GSM4146776 OTHER 2.0 MB
SRR10384093_GSM4146777 OTHER 16.0 MB
SRR10384094_GSM4146778 OTHER
SRR10384095_GSM4146779 OTHER
SRR10384096_GSM4146780 OTHER
SRR10384097_GSM4146781 OTHER 1.0 MB
SRR10384098_GSM4146782 OTHER
SRR10384099_GSM4146783 OTHER
SRR10384100_GSM4146784 OTHER
SRR10384101_GSM4146785 OTHER
SRR10384102_GSM4146786 OTHER
SRR10384103_GSM4146787 OTHER
SRR10384104_GSM4146788 OTHER
SRR10384105_GSM4146789 OTHER
SRR10384106_GSM4146790 OTHER 1.0 MB
SRR10384107_GSM4146791 OTHER
SRR10384108_GSM4146792 OTHER 1.0 MB
SRR10384109_GSM4146793 OTHER
SRR10384110_GSM4146794 OTHER
SRR10384111_GSM4146795 OTHER 4.0 MB
SRR10384112_GSM4146796 OTHER 33.0 MB
SRR10384113_GSM4146797 OTHER
SRR10384114_GSM4146798 OTHER
SRR10384115_GSM4146799 OTHER
SRR10384116_GSM4146800 OTHER 1.0 MB
SRR10384117_GSM4146801 OTHER 1.0 MB
SRR10384118_GSM4146802 OTHER 1.0 MB
SRR10384119_GSM4146803 OTHER
SRR10384120_GSM4146804 OTHER 12.0 MB
SRR10384121_GSM4146805 OTHER
SRR10384122_GSM4146806 OTHER 1.0 MB
SRR10384123_GSM4146807 OTHER
SRR10384124_GSM4146808 OTHER 6.0 MB
SRR10384125_GSM4146809 OTHER 3.0 MB
SRR10384126_GSM4146810 OTHER 2.0 MB
SRR10384127_GSM4146811 OTHER 1.0 MB
SRR10384128_GSM4146812 OTHER
SRR10384129_GSM4146813 OTHER 1.0 MB
SRR10384130_GSM4146814 OTHER 6.0 MB
SRR10384131_GSM4146815 OTHER
SRR10384132_GSM4146816 OTHER 7.0 MB
SRR10384133_GSM4146817 OTHER 6.0 MB
SRR10384134_GSM4146818 OTHER
SRR10384135_GSM4146819 OTHER 10.0 MB
SRR10384136_GSM4146820 OTHER 1.0 MB
SRR10384137_GSM4146821 OTHER
SRR10384138_GSM4146822 OTHER
SRR10384139_GSM4146823 OTHER
SRR10384140_GSM4146824 OTHER 2.0 MB
SRR10384141_GSM4146825 OTHER 1.0 MB
SRR10384142_GSM4146826 OTHER 10.0 MB
SRR10384143_GSM4146827 OTHER
SRR10384144_GSM4146828 OTHER
SRR10384145_GSM4146829 OTHER 4.0 MB
SRR10384146_GSM4146830 OTHER
SRR10384147_GSM4146831 OTHER
SRR10384148_GSM4146832 OTHER 4.0 MB
SRR10384149_GSM4146833 OTHER
SRR10384150_GSM4146834 OTHER
SRR10384151_GSM4146835 OTHER 1.0 MB
SRR10384152_GSM4146836 OTHER
SRR10384153_GSM4146837 OTHER
SRR10384154_GSM4146838 OTHER
SRR10384155_GSM4146839 OTHER
SRR10384156_GSM4146840 OTHER
SRR10384157_GSM4146841 OTHER
SRR10384158_GSM4146842 OTHER 4.0 MB
SRR10384159_GSM4146843 OTHER
SRR10384160_GSM4146844 OTHER
SRR10384161_GSM4146845 OTHER 1.0 MB
SRR10384162_GSM4146846 OTHER
SRR10384163_GSM4146847 OTHER
SRR10384164_GSM4146848 OTHER 4.0 MB
SRR10384165_GSM4146849 OTHER
SRR10384166_GSM4146850 OTHER
SRR10384167_GSM4146851 OTHER
SRR10384168_GSM4146852 OTHER 35.0 MB
SRR10384169_GSM4146853 OTHER
SRR10384170_GSM4146854 OTHER 2.0 MB
SRR10384171_GSM4146855 OTHER 1.0 MB
SRR10384172_GSM4146856 OTHER
SRR10384173_GSM4146857 OTHER 7.0 MB
SRR10384174_GSM4146858 OTHER
SRR10384175_GSM4146859 OTHER
SRR10384176_GSM4146860 OTHER 6.0 MB
SRR10384177_GSM4146861 OTHER 48.0 MB
SRR10384178_GSM4146862 OTHER 1.0 MB
SRR10384179_GSM4146863 OTHER 2.0 MB
SRR10384180_GSM4146864 OTHER 5.0 MB
SRR10384181_GSM4146865 OTHER
SRR10384182_GSM4146866 OTHER
SRR10384183_GSM4146867 OTHER
SRR10384184_GSM4146868 OTHER
SRR10384185_GSM4146869 OTHER
SRR10384186_GSM4146870 OTHER
SRR10384187_GSM4146871 OTHER
SRR10384188_GSM4146872 OTHER
SRR10384189_GSM4146873 OTHER 1.0 MB
SRR10384190_GSM4146874 OTHER
SRR10384191_GSM4146875 OTHER 5.0 MB

Potentially related datasets 1

These accessions were text-mined from the PMC full text. They may be referenced for comparison, cited from other studies, or otherwise mentioned without being primary data for this paper.

Accession Source Title
GSE139815 GSE · GEO GEO ↗ Pooled CRISPR screens with imaging on microRaft arrays reveals stress granule-regulatory factors

Analysis pipelines 1

Pipeline Assay Steps Dataset
GSE139815 Data Processing geo_data_processing — 2 GSE139815
Funding 10 grants
Grant Funder
R01 HG004659 NHGRI NIH HHS (United States)
U54 CA209891 NCI NIH HHS (United States)
R01 NS103172 NINDS NIH HHS (United States)
T32 GM145427 NIGMS NIH HHS (United States)
T32 GM008666 NIGMS NIH HHS (United States)
P50 GM085764 NIGMS NIH HHS (United States)
K99 HG009530 NHGRI NIH HHS (United States)
F31 CA217173 NCI NIH HHS (United States)
F31 CA206233 NCI NIH HHS (United States)
R01 EY024556 NEI NIH HHS (United States)